1PPK

CRYSTALLOGRAPHIC ANALYSIS OF TRANSITION STATE MIMICS BOUND TO PENICILLOPEPSIN: PHOSPHOROUS-CONTAINING PEPTIDE ANALOGUES

Structural Biology Knowledgebase: 1PPK SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Observed: 0.132

Literature

Macromolecules
Sequence Display for 1PPK

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 34488.17

Macromolecule Entities
Molecule Chains Length Organism Details
PENICILLOPEPSIN E 323 Penicillium janthinellum EC#: 3.4.23.20 IUBMB
Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
IVV
Query on IVV

E N-(3-methylbutanoyl)-L-valyl-N-{(1R)-1-[(R)- (2-ethoxy-2-oxoethyl)(hydroxy)phosphoryl]- 3-methylbutyl}-L-valinamide
PHOSPHINIC ACID ANALOGUE OF STATIN (IVA)- VAL-VAL-STA(P)-O-ET (Synonym)
C24 H46 N3 O7 P
GSDBAIBPJKAZKN-HJNYFJLDSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MAN
Query on MAN

E ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
HSY
Query on HSY

E alpha-L-xylopyranose
C5 H10 O5
SRBFZHDQGSBBOR-SKNVOMKLSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

E SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
DMF
Query on DMF

E DIMETHYLFORMAMIDE
C3 H7 N O
ZMXDDKWLCZADIW-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
IVV N/A in BindingDB
Ki: 22 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Observed: 0.132
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 97.48 α = 90.00
b = 46.55 β = 116.14
c = 66.42 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1994-01-20
  • Released Date: 1994-05-31
  • Deposition author(s): Strynadka, N.C.J., James, M.N.G.

Revision History

  • 2012-12-12
    Type: Other | Details: Add PRD info
  • 2011-07-13
    Type: Atom nomenclature | Details: Atom nomenclature
  • 2011-07-13
    Type: Binding sites and description | Details: Binding sites and description
  • 2011-07-13
    Type: Non-polymer description | Details: Non-polymer description
  • 2011-07-13
    Type: Function and keywords | Details: Function and keywords
  • 2011-07-13
    Type: Linkage | Details: Linkage
  • 2011-07-13
    Type: Sequence database correspondence | Details: Sequence database correspondence
  • 2011-07-13
    Type: Polymer description | Details: Changed inhibitor presentation or chemistry
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4